Parasite 2014, 21, 69
Ó A. Charbonnier et al., published by EDP Sciences, 2014
DOI: 10.1051/parasite/2014075
Available online at:
A new data management system for the French National Registry
of human alveolar echinococcosis cases
Amandine Charbonnier1,2, Jenny Knapp1,3,*, Florent Demonmerot1,3, Solange Bresson-Hadni1,3,
Francis Raoul1,3, Frédéric Grenouillet1,3, Laurence Millon1,3, Dominique Angèle Vuitton1,3,
and Sylvie Damy1
Laboratoire Chrono-Environnement, UMR/CNRS 6249 University of Franche-Comté, 25000 Besançon, France
OSU THETA Franche-Comté Bourgogne, 25000 Besançon, France
National Reference Centre of Alveolar Echinococcosis – FrancEchino Network – WHO Collaborating Centre for Prevention
and Treatment of Human Alveolar Echinococcosis, University Hospital Centre of Besançon, 25000 Besançon, France
Received 29 October 2014, Accepted 12 December 2014, Published online 22 December 2014
Abstract – Alveolar echinococcosis (AE) is an endemic zoonosis in France due to the cestode Echinococcus
multilocularis. The French National Reference Centre for Alveolar Echinococcosis (CNR-EA), connected to the
FrancEchino network, is responsible for recording all AE cases diagnosed in France. Administrative, epidemiological
and medical information on the French AE cases may currently be considered exhaustive only on the diagnosis time.
To constitute a reference data set, an information system (IS) was developed thanks to a relational database management system (MySQL language). The current data set will evolve towards a dynamic surveillance system, including
follow-up data (e.g. imaging, serology) and will be connected to environmental and parasitological data relative to
E. multilocularis to better understand the pathogen transmission pathway. A particularly important goal is the possible
interoperability of the IS with similar European and other databases abroad; this new IS could play a supporting role
in the creation of new AE registries.
Key words: Alveolar echinococcosis, Registry, Database, Interoperability of data.
Résumé – Un nouveau système de base de données pour le registre national français des cas humains
d’échinococcose alvéolaire. L’échinococcose alvéolaire (EA) est une zoonose endémique en France,
due au cestode Echinococcus multilocularis. Le Centre National de Référence français de l’échinococcose
alvéolaire (CNR-EA), lié au réseau FrancEchino est en charge de l’enregistrement de tous les cas d’EA
diagnostiqués en France. Les informations administratives, épidémiologiques et médicales sur les cas d’EA
français ne sont actuellement exhaustives que pour la période du diagnostic. Dans le but de constituer un jeu de
données de référence, un système d’information (SI) a été développé grâce à un système de gestion de base de
données relationnelle (langage MySQL). L’actuel jeu de données évoluera vers un système de surveillance
dynamique, prenant en compte les données de suivi (par exemple, données d’imagerie, sérologie) et sera connecté
à des données environnementales et parasitologiques, relatives à E. multilocularis, pour mieux comprendre les
voies de transmission du pathogène. Un point particulièrement important ici est la possibilité du SI d’être
interopérable avec d’autres bases de données similaires, en Europe et ailleurs ; ce nouveau SI pourrait donc
servir de support à la création de nouveaux registres de l’EA.
Alveolar echinococcosis (AE) is a rare but severe endemic
zoonosis due to the cestode Echinococcus multilocularis,
commonly named the fox tapeworm. The main actors of the
sylvatic cycle are carnivores (e.g. fox and dogs) as definitive
hosts, which harbour the adult stage in their small intestine,
and voles and lagomorphs as intermediate hosts, which harbour the larval stage mainly in the liver [19]. Humans are
infected by eating raw vegetables or by contact with soil or
*Corresponding author: [email protected]
Innovation for the Management of Echinococcosis.
Invited editors: Dominique A. Vuitton, Laurence Millon, Bruno Gottstein and Patrick Giraudoux
This is an Open Access article distributed under the terms of the Creative Commons Attribution License (,
which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
A. Charbonnier et al.: Parasite 2014, 21, 69
carnivore fur contaminated by the parasite eggs [3]. Domestic
carnivores can be involved in the parasite cycle and their close
contact with humans increases the risk of parasite transmission
[17]. The diagnosis of AE can only be performed several years
after the contact with the parasite due to a long asymptomatic
period [1]. The occurrence of the disease in humans is considered a multifactorial event. Different environmental and behavioural factors are suspected to be responsible for the infection,
such as activity in agriculture, hunting or close contact with
carnivores [9]. The marked increase in the fox population in
Europe and the presence of foxes in the cities have increased
the probability of contact with the parasite within the last three
decades, as demonstrated in Switzerland [16]. Along with such
external risk factors, new host-linked risks are emerging such
as the high incidence rate of AE in immunosuppressed
patients, suggesting an opportunistic status for the parasite
[4]. The delay between first contact and diagnosis and the multifactorial causes of disease occurrence emphasize the complexity of diagnosis and the possibility of epidemiological
changes over time. In most regions, disease incidence is low,
and changes may either remain unnoticed or be misinterpreted
at a single centre level by hospitals out of the endemic region.
This would justify permanent population-based surveillance of
the disease at a continental level. However, after a first attempt
at establishing an observatory of cases at the European level,
the EurEchinoReg project [9], and despite the inclusion of
echinococcosis among those zoonoses that should be reported
to the European CDC (Centre For Disease Control) and EFSA
(European Food Safety Authority), AE surveillance is currently
performed in each state and is rather heterogeneous in its organization and reliability [7].
In France the historical endemic area is represented, for
human cases, by the eastern regions and the mountains of
Massif Central; 22 French administrative divisions named
départements at risk (DAR) of human infection by E. multilocularis have been defined [12]. The annual incidence is 0.026
new cases per 100,000 inhabitants (at the country level), and
in 2003, French cases represented 42% of the total number of
collected cases in Europe [9, 14]. Since 1997, the WHOCollaborating Centre for Prevention and Treatment of Human
Echinococcosis, located in Besançon, France, at the Regional
and University Hospital Centre (CHRUB), has recorded the
human cases of AE diagnosed on the French territory retrospectively for 1982–1996, then prospectively afterwards [9].
Since 2004, using different data management software types,
data collection was performed within the framework of an
agreement between the French Institute for Public Health
Surveillance (Institut de Veille Sanitaire, InVS) and the
FrancEchino network, and in 2012 it became part of the missions given by the InVS to the National Reference Centre
for Alveolar Echinococcosis (Centre National de Référence
de l’Échinococcose Alvéolaire, CNR-EA). This comprehensive
recording of AE cases has allowed the FrancEchino registry to
serve as a reliable basis for epidemiological and clinical studies
[4, 9, 11, 12]. Although there is no legal notification of AE
cases in France, the aim of the FrancEchino registry is to
record all AE cases diagnosed in France on a population-basis
and in a most exhaustive manner. This is achieved through
active investigation thanks to collaborations between the
CHRUB and hospital centres from the eastern, northern and
central parts of France (FrancEchino Network), and by yearly
requests to hospital pharmacies in charge of supplying
EskazoleÒ (albendazole), the only drug available to treat the
disease, as well as to Pathology and Parasitology laboratories.
Communication between the FrancEchino network partners
and non-specialists in AE among health professionals all over
France improves the awareness of all actors about AE and its
presentation in patients. In addition to its surveillance role,
the AE monitoring system may thus participate in decreasing
the time to AE diagnosis in non-endemic regions and in
improving the care management of patients. To achieve its
objectives, the FrancEchino registry must adopt strict rules
and be structured around a universal system taking into
account the complex clinical and environmental aspects of
AE, by integrating new data (such as co-morbidities) and must
be able to connect to environmental data relevant for transmission (e.g. prevalence of E. multilocularis in foxes, landscape
features). This has led us to move from the existing simple data
file systems to a new efficient, secure and easy-to-use database
which would allow the quality control of recorded data, the
standardization of patient enrolment and follow-up, the integration of ecological and environmental data, and the targeted
consultation of the data based on different types of users. This
paper aims to describe the design of this new IS, to highlight
the methodological issues, and to discuss its possible extension
to other countries for integrated surveillance of AE in endemic
regions of the world.
Materials and methods
As the design of the AE registry information system (IS) is
geared towards disease surveillance and clinical monitoring, as
well as data use in scientific research, such a system should not
be fixed and must be able to evolve over time. For that reason,
we used a process called ‘‘separation of concerns (SoC)’’ [6]
for the development of the IS. This approach separates what
is to be done from how it is to be done. Through proper separation of concerns, complexity becomes manageable.
The first step was to describe all AE key data collected for
the registry as patient data, medical data, epidemiological data,
etc., using a conceptual model. This step required close collaboration between data managers and people in charge of modelling the current key data. The database model (i.e. the
relational framework) was completed within 4 months. As it
was at the beginning of our work, the documented data sets
included three parts: administrative (identity, age of the patient
at the time of diagnosis, sex, etc.), epidemiological (geographical location, risk factors such as trips to endemic regions,
activity in agriculture, hunting, owning dogs and cats, etc.),
and medical information (diagnosis date, medical and surgical
history, location of the parasite lesions, surgery and drug treatment, occurrence and location of metastases, etc.).
Meanwhile, specific research projects had been implemented, which required both a common background of epidemiological and clinical data already accessible from the
registry database and dedicated ‘‘modules’’ that could be
annexed to the general background. In addition, possible
A. Charbonnier et al.: Parasite 2014, 21, 69
Figure 1. The main data parts of the information system for the FrancEchino human cases registry.
extension to other research teams had to be taken into account.
This first step also required clear definition of the roles of each
user who could have access to the IS.
The second step was the development of the IS itself, taking the needs of users into account. The IS integrates a data
management system and a web application. Its use in the area
of scientific research has forced the application to be developed
in a scalable manner, using technologies maintained over the
long term. Thus, the relational database management system
(RDBMS) MySQL was used to implement the database, an
open-source RDBMS widely used in the world. The web application was developed in PHP and JavaScript.
To extract master data, that represent the entities which
were agreed upon and are shared across the scientific community of AE case management, we used processes of Master
Data Management (MDM) [13]. When merging the previous
master data and those required in the new IS, we removed
duplicates, standardized data, and incorporated rules to eliminate incorrect data from entering the system in order to create
a reliable source of master data.
The application of the MDM has permitted us to introduce
reference data in the IS. They are used to define a set of permissible values for fields, the majority of them being defined
by standards from organizations at the national level, such as
country codes as defined in ISO 3166-1 or French département
codes as defined in the COG (for ‘‘Code Officiel Géographique’’), the geographical official code of the INSEE (for ‘‘Institut National de la Statistique et des Études Économiques’’), the
French national institute of statistics and economic studies.
The usage of standard reference data is a way to improve database interoperability. Some reference data were recovered from
other databases, like organs which are the same as in tumour
registries, such as the Tumour Registry of the Doubs département, another registry linked to the InVS and operated in the
same hospital (CHRUB).
A data conceptual model was built with MERISE (an analysis and modelling methodology for information system development [2]). The model is composed of groups of main data
parts (Fig. 1), e.g. patient (administrative data), epidemiological data and medical data. It provides new features like history
of AE course in patients, associated diseases, care management
and follow-up in terms of serology and imaging that are crucial
both for diagnosis, classification and follow-up, and treatments
(including surgery, medical treatment and side effects).
A database scheme was designed, allowing us to take the
integration of new data types into account. If shared in the
future by several research teams, depending on the level of precision case retrieval may reach, the system will allow users to
define the common vs. specific items, and to analyse data in
common or separately.
To guarantee accuracy (i.e. exhaustivity and absence of
double recording), the registry contains patients’ names and
personal data, and there are strict requirements by French
national laws to secure their access (http://www.;jsessionid=E0BCC13BFE62F
00006052581&dateTexte=20140721; Compliance with the recommendations of the two official French
ethics committees for personal data protection has to be ensured
to obtain the required authorizations to maintain a disease registry
using people’s full names and addresses. These are the CNIL (for
‘‘Commission Nationale de l’Informatique et des Libertés’’), the
French data protection authority, and the CPP (for ‘‘Comité de
Protection des Personnes’’), the regional committee for patients’
legal protection. The IS thus includes many levels of security:
on the web server, on the database and on the web application with
a user management system. The user management system is based
A. Charbonnier et al.: Parasite 2014, 21, 69
Figure 2. User-friendly interface: screen capture of the form accessible to the user (health professional in charge of patient) to add a patient’s
on roles formerly defined to use the registry but it is flexible
because the architecture is based on Role-Based Access Control
(RBAC) [15]. This method permitted us to define all required roles
and permissions to manage user privileges. The current user management system offers three types of access: public access, FrancEchino network (or any similar type of professional network)
physician access and data manager access. (1) ‘‘Public access’’
provides statistics, charts and maps for users. These charts and
maps are automatically generated from data. (2) ‘‘FrancEchino
network physician access’’ is available with an authentication by
login and password and it offers anonymous lists of patients.
(3) ‘‘Data manager access’’ is available with an authentication
by login and password. It allows data managers to enter new data
in the database after proper validation for accuracy, and to access
all data. Data input by a data manager is validated beforehand by a
specialist in AE, according to the procedures agreed upon between
the CNR-EA and the InVS. When a data manager includes a new
patient, the IS provides a form with inputs (Fig. 2). The data manager has to fill in or select reference data from a list. The records of
a form are only possible if all mandatory data are filled in and if
rules are checked. This new way of including a patient in the registry is easier, with a user-friendly GUI (Graphical User Interface),
and it simplifies the process of data homogenization. Overall, this
step improves the process of data validation. Since the anonymous
data are available by authorized persons, complete non-anonymous data are exclusively localized on a local server, specifically
protected from any intrusion according to the CNIL’s
Zoonoses are complex diseases which combine animal and
human hosts, as well as key environmental or anthropic factors
which are continuously changing with time [5, 10]. An integrated system of data collection and recording must take all
these aspects into account. The data management system that
has been developed to improve data collection by the
A. Charbonnier et al.: Parasite 2014, 21, 69
FrancEchino registry, in addition to complying with French
National regulations, which are particularly strict, satisfies this
scientific requirement and could serve as a basis for the establishment of a European or multinational registry of AE.
Applying the principle of separation of concerns to IS
design results in a number of benefits such as the increase in
maintainability and extensibility that can have a major impact
on the adoption rate of the system. The division into components that focus on a single purpose, leads to the definition
and use of components that are more easily reused in other systems, or different contexts within the same system. This principle helps users in the management of complexity by
eliminating unnecessary duplication and proper responsibility
allocation in entities.
The current IS provides many possibilities to export data:
export to the InVS using the InVS format in spreadsheets, multicriteria export in standard formats such as ‘‘csv’’ format.
It also enables export of charts for completing annual reports
both at the National and European levels of AE surveillance.
On the web application, guidelines on epidemiological and
medical data registration will be provided to facilitate the
assessment and recording of new cases and addition of data
by data managers and FrancEchino physicians, with online
access to registry codes. The IS will be online by early 2015.
Along with the functionalities dedicated to clinical management and epidemiological surveillance in humans, the possibility of a specific development of this system towards the
inclusion of specific research-orientated data is under study.
AE is a rare disease, and for each endemic country, the
quantity of data is not a limiting factor for the choice of the
system in use. The number of French human cases recorded
in the FrancEchino registry with a diagnosis of AE between
January 1982 and December 2013 was 575 (CNR-EA data).
The highest incidence rates in France are currently recorded
in five départements (Doubs, Haute-Saône, Jura, Vosges and
Haute-Savoie) with an annual incidence higher than two new
cases per 100,000 inhabitants, which represents 60% of cases
recorded in France. Treatment and monitoring of the disease
in humans, with long-term follow-up, represent a significant
economic burden for countries [18], because of the long-term
treatment and costly procedures such as liver transplantation.
Long-term follow-up of each patient is therefore a factor for
the incremental increase of data with time. Patient management and treatment need to be harmonized between clinical
centres in Europe, as was emphasized recently [8]. A key
objective was thus to develop an AE registry with standardized
protocols, master and reference data to allow harmonized data
management and research on AE epidemiology first at a
European then at world level. The IS we developed well fits
with such a requirement. At the time of writing this article,
sharing this IS to include AE data from Germany is scheduled.
As Germany is a traditionally endemic area with the second
largest set of data regarding AE and new emerging characteristics (spreading of fox and human infection over the country,
possible transmission of the parasite from foxes to humans in
cities. . .), this common IS could become the core system for
AE surveillance in Europe. Adoption of the same database system to record cases in the most endemic areas of China is also
planned. A meeting of all interested groups involved in AE
surveillance is scheduled for April 2015; at this meeting, final
decisions on points still debated, for instance on shared key
definitions (date of diagnosis, imaging classification in addition
to PNM classification – parasite lesion, neighbouring organ
invasion, metastases) and procedures for case-recording and
cross-confirmation of cases to reach completeness, adapted
to each country, should be agreed upon.
Acknowledgements. The authors deeply thank Prof. Patrick
Giraudoux for his constant support to a multidisciplinary approach
of alveolar echinococcosis epidemiology, Prof. Georges Mantion
and Dr. Carine Richou as well as all members of the FrancEchino
network for their precious help in the implementation of the
FrancEchino Registry since 1997, and Dr. Beate Grüner and
Tilmann Graeter for their interest in our endeavour.
1. Ammann RW, Eckert J. 1996. Cestodes. Echinococcus.
Gastroenteroly clinics of North America, 25, 655–689.
2. Avison D. 1991. MERISE: A European methodology for
developing information systems. European Journal of Information Systems, 1(3), 183–191.
3. Bresson-Hadni S, Piarroux R, Bartholomot B, Miguet J,
Mantion G, Vuitton D. 2005. Échinococcose alvéolaire –
Alveolar echinococcosis. EMC – Hépato-Gastroentérologie, 2,
4. Chauchet A, Grenouillet F, Knapp J, Richou C, Delabrousse E,
Dentan C, Millon L, Di Martino V, Contreras R, Deconinck E,
Blagosklonov O, Vuitton D-A, Bresson-Hadni S, FrancEchino
Network. 2014. Increased incidence and characteristics of
alveolar echinococcosis in patients with immunosuppressionassociated conditions. Clinical Infectious Diseases, 59,
5. Davidson RK, Romig T, Jenkins E, Tryland M, Robertson LJ.
2012. The impact of globalisation on the distribution of Echinococcus multilocularis. Trends in Parasitology, 28, 239–247.
6. Frankel DS. 2003. Model driven Architecture – Applying MDA to
Enterprise Computing. OMG Press, Wiley Publishing: New York.
7. Jorgensen P, Van der Heiden M, Kern P, Schöneberg I, Krause G,
Alpers K. 2008. Underreporting of human alveolar echinococcosis, Germany. Emerging Infectious Diseases, 14(6), 935–937.
8. Junghanss T. 2014. Clinical management of echinococcosis
needs attention as long as control fails, European Scientific
Counsel Companion Animal Parasites Echinococcus 2014
Symposium, Vilnius, October, 8–9.
9. Kern P, Bardonnet K, Renner E, Auer H, Pawlowski Z,
Ammann RW, Vuitton D-A, Kern P, European Echinococcosis
Registry. 2003. European echinococcosis registry: human
alveolar echinococcosis, Europe, 1982–2000. Emerging Infectious Diseases, 9, 343–349.
10. Morse SS. 1995. Factors in the emergence of infectious
diseases. Emerging Infectious Diseases, 1, 7–15.
11. Piarroux M, Piarroux R, Giorgi R, Knapp J, Bardonnet K,
Sudre B, Watelet J, Dumortier J, Gérard A, Beytout J, Abergel A,
Mantion G, Vuitton D-A, Bresson-Hadni S. 2011. Clinical
features and evolution of Alveolar Echinococcosis in France from
1982 to 2007: results of a survey in 387 patients. Journal of
Hepatology, 55, 1025–1033.
A. Charbonnier et al.: Parasite 2014, 21, 69
12. Piarroux M, Piarroux R, Knapp J, Bardonnet K, Dumortier J,
Watelet J, Gerard A, Beytout J, Abergel A, Bresson-Hadni S,
Gaudart J, FrancEchino Surveillance Network. 2013. Populations at risk for alveolar echinococcosis, France. Emerging
Infectious Diseases, 19, 721–728.
13. Régnier-Pécastaing F, Gabassi M, Finet J. 2008. MDM, Enjeux
et méthodes de la gestion des données. Dunod: Paris.
14. Said-Ali Z, Grenouillet F, Knapp J, Bresson-Hadni S, Vuitton
D-A, Raoul F, Richou C, Millon L, Giraudoux P, Francechino
Network. 2013. Detecting nested clusters of human alveolar
echinococcosis. Parasitology, 140, 1693–1700.
15. Sandhu R, Ferraiolo DF, Kuhn R. 2000. The NIST model for
role based access control: Toward a unified standard – first
public draft of the NIST RBAC model and proposal for an
RBAC standard, 5th ACM Workshop on Role Based Access
Control, Berlin, July 26–27.
16. Schweiger A, Ammann RW, Candinas D, Clavien P-A, Eckert J,
Gottstein B, Halkic N, Muellhaupt B, Prinz BM, Reichen J, Tarr
PE, Torgerson PR, Deplazes P. 2007. Human alveolar echinococcosis after fox population increase, Switzerland. Emerging
Infectious Diseases, 13, 878–882.
17. Thompson RC, McManus DP. 2001. Aetiology: parasites and
life-cycles, in Manual WHO/OIE on Echinococcosis in
Humans and Animals: A Public Health Problem of Global
Concern. Eckert J, Gemmell M, Meslin FX, Pawlowski Z,
Editors. World Organisation for Animal Health: Paris. p. 1–19.
18. Torgerson PR, Keller K, Magnotta M, Ragland N. 2010. The
global burden of alveolar echinococcosis. PLoS Neglected
Tropical Diseases, 4, e722.
19. Vuitton D-A, Zhou H, Bresson-Hadni S, Wang Q, Piarroux M,
Raoul F, Giraudoux P. 2003. Epidemiology of alveolar echinococcosis with particular reference to China and Europe.
Parasitology, 127, S87–S107.
Cite this article as: Charbonnier A, Knapp J, Demonmerot F, Bresson-Hadni S, Raoul F, Grenouillet F, Millon L, Vuitton DA & Damy S:
A new data management system for the French National Registry of human alveolar echinococcosis cases. Parasite, 2014, 21, 69.
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